The USDA's Wildlife Services Program, which contracts with farmers for bird control, said it used an avicide poison called DRC-1339 to cull a roost of 5,000 birds that were defecating on a farmer's cattle feed across the state line in Nebraska. But officials said the agency had nothing to do with large and dense recent bird kills in Arkansas and Louisiana.

Nevertheless, the USDA's role in the South Dakota bird deaths puts a focus on a little-known government bird-control program that began in the 1960s under the name of Bye Bye Blackbird, which eventually became part of the USDA and was housed in the late '60s at a NASA facility. In 2009, USDA agents euthanized more than 4 million red-winged blackbirds, starlings, cowbirds, and grackles, primarily using pesticides that the government says are not harmful to pets or humans.

In addition to the USDA program, a so-called depredation order from the US Fish and Wildlife Service allows blackbirds, grackles, and starlings to be killed by anyone who says they pose health risks or cause economic damage. Though a permit is needed in some instances, the order is largely intended to cut through red tape for farmers, who often employ private contractors to kill the birds and do not need to report their bird culls to any authority.

"Every winter, there's massive and purposeful kills of these blackbirds," says Greg Butcher, the bird conservation director at the National Audubon Society. "These guys are professionals, and they don't want to advertise their work. They like to work fast, efficiently, and out of sight."

Bird kills turning too zealous?

The depredation order, however, is under review for its impact on the rare rusty blackbird, which roosts with more common species. Ornithologists also suspect that the mass killings may be a factor in declining populations of those species in the US.

While the USDA keeps tabs on the number of birds the program euthanizes, the total death toll isn't known because private contractors operating under the depredation order aren't required to keep count in the case of blackbirds, cowbirds, grackles, and starlings.

"My biggest concern is we don't know how many birds are being killed, and we don't have a sense of how at risk the rusty blackbird is because of depredation events in their range," says Mr. Butcher.

Yankton animal control officer Lisa Brasel told KTIV-TV that she first believed a cold snap had killed some 200 European starlings that were found dead in Riverside Park, reminding some residents of the final scenes of Alfred Hitchcock's thriller, "The Birds."

But then she said she received a call from a USDA official who said the agency had poisoned a roost of starlings 10 miles south of Yankton. Usually such poisonings result in flocks falling directly out of their tree roosts. But in this case, the birds traveled a fair distance before falling. "They were surprised they came to Yankton like they did and died in our park," said Brasel, according to KTIV-TV.

How birds plague farmers

Carol Bannerman, a Wildlife Services spokeswoman, said such kills are carried out at the request of farmers who can prove the birds are a nuisance. The farmers also help pay the cost, according to the agency.

One example of nuisance birds are European starlings, a non-native species, at US dairies, where a flock of 5,000 can eat 200 pounds of feed a day while soiling equipment and dairy cows.

"It's not that we have anything against starlings, but our charge is to help protect agriculture ... and protect property and human health or safety," she says. "And the fact is, in a lot of rural settings, people say, 'It's just birds, what's the problem?' "

Ms. Bannerman added, however, that the agency takes care to notify local public-health and law-enforcement agencies before a scheduled kill, and noted "what went on in Louisiana and Arkansas, that was totally outside of what we're doing. We're quite concerned that people not connect those."

Two mass bird deaths in north Alabama this week are being investigated, with specimens being tested for toxicity. Two other mass bird deaths in Gilbertville and Murray, Ky., earlier this month were not linked to poison, but could have been caused by unseasonably cold weather. The most widely reported recent mass bird deaths – in Louisiana and Arkansas – have been tied to birds en masse flying into buildings and power lines.

Rogue fireworks in Arkansas

In Arkansas, state ornithologist Karen Rowe has reviewed ground radar records that show a 20,000-plus bird roost taking flight at approximately 10:15 p.m. on New Year's Eve, 15 minutes after a series of large booms shook the windows of houses in a nearby subdivision.

This has caused state wildlife officials to pin the blame on a resident who may have gotten a hold of professional-grade fireworks. The dead birds were likely animals that were trying to land in the dark and hit some kind of object after being drawn to toward the artificial light of the neighborhood.

"So far, no one has confessed to letting off the fireworks, but the question remains if anyone would admit to it," says Ms. Rowe. They needn't fear retribution. Despite the number of birds that died, no laws were broken.

Some 5 billion birds die every year across the US, most largely unnoticed. Mass deaths are not uncommon. The US Geological Service's website listed about 90 mass deaths of birds and other wildlife in the last six months of 2010.

"Whether people are noticing it more and pointing it out more this year than in the past, is something that I'd be thinking about," says Bannerman at the USDA.